Update ipynbname. Update openmpi version to replace from /apps. Add s… #46
Workflow file for this run
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| name: Build and test conda env | |
| on: pull_request | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| ### Latest at time of writing | |
| uses: actions/checkout@v3.3.0 | |
| - name: Sync repository to Gadi | |
| ### Latest at time of writing | |
| uses: up9cloud/action-rsync@v1.3 | |
| env: | |
| HOST: gadi.nci.org.au | |
| TARGET: ${{secrets.GADI_REPO_PATH}} | |
| KEY: ${{secrets.DEPLOY_KEY}} | |
| USER: ${{secrets.GADI_USER}} | |
| - name: Create Admin dirs on Gadi | |
| uses: appleboy/ssh-action@v0.1.7 | |
| with: | |
| host: gadi.nci.org.au | |
| username: ${{secrets.GADI_USER}} | |
| key: ${{secrets.DEPLOY_KEY}} | |
| script: | | |
| source ${{secrets.GADI_REPO_PATH}}/scripts/install_config.sh | |
| source ${{secrets.GADI_REPO_PATH}}/scripts/functions.sh | |
| mkdir -p $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR | |
| set_admin_perms $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR | |
| - name: Build environment | |
| uses: appleboy/ssh-action@v0.1.7 | |
| with: | |
| host: gadi.nci.org.au | |
| username: ${{secrets.GADI_USER}} | |
| key: ${{secrets.DEPLOY_KEY}} | |
| command_timeout: 120m | |
| script: | | |
| export SCRIPT_DIR=${{secrets.GADI_REPO_PATH}}/scripts | |
| eval $( grep ADMIN_DIR $SCRIPT_DIR/install_config.sh ) | |
| eval $( grep JOB_LOG_DIR $SCRIPT_DIR/install_config.sh ) | |
| cd $JOB_LOG_DIR | |
| qsub -N build_conda -lncpus=1,mem=20GB,walltime=2:00:00,jobfs=50GB,storage=gdata/v45+scratch/v45+gdata/hh5+scratch/hh5 -v SCRIPT_DIR -P kr06 -q copyq -Wblock=true -Wumask=037 "${SCRIPT_DIR}"/build.sh | |
| test: | |
| needs: build | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Test environment | |
| uses: appleboy/ssh-action@v0.1.7 | |
| with: | |
| host: gadi.nci.org.au | |
| username: ${{secrets.GADI_USER}} | |
| key: ${{secrets.DEPLOY_KEY}} | |
| script: | | |
| export SCRIPT_DIR=${{secrets.GADI_REPO_PATH}}/scripts | |
| eval $( grep ADMIN_DIR $SCRIPT_DIR/install_config.sh ) | |
| eval $( grep JOB_LOG_DIR $SCRIPT_DIR/install_config.sh ) | |
| cd $JOB_LOG_DIR | |
| qsub -N test_conda -lncpus=4,mem=20GB,walltime=0:20:00,jobfs=50GB,storage=gdata/v45+scratch/v45+gdata/hh5+scratch/hh5 -v SCRIPT_DIR -P kr06 -Wblock=true -Wumask=037 "${SCRIPT_DIR}"/test.sh |